How To¶

This section provides answers to frequent questions, that looks easy to answer, but that requires digging somewhat deeper into the documentation.

General issues¶

How to convert an SVG file produced by VL to another format?¶

The easiest way is to use Inkscape [1] program. The conversion can be done from command line:

# on MacOS
~/bin/Inkscape.app/Contents/MacOS/inkscape plot.svg --export-filename=plot.png -d 500

# on Windows
inkscape "C:\path\plot.svg" --export-filename="C:\path\plot.png"

# on Linux
inkscape -z -e plot.png -w 1000 -d 500 plot.svg

Questions regarding plotting¶

How to adjust data range on a plot?¶

Data range is set by Plot class constructor, e.g.

pl = Plot(drawing,200,1000,200,1000,0.0,110.0,0.0,150.0,axes_definition="UBLR")
pl.bars(x_data, y_data, adjust_range=False)

where the plotting area is a square 800x800 (from 200 to 1000 along each direction) and data range on X and Y axes are [0, 110.0] and [0.0, 150.0], respectively. These ranges can be also set after a Plot object has been constructed:

pl.axes["B"].min_data_value = 0
pl.axes["B"].max_data_value = 15

This will affect bottom axis (because of B). Remember to switch off automatic data range assignment by setting adjust_range=False kwarg argument when plotting.

Questions regarding widgets¶

How to download a PDB file?¶

Use AjaxCommunication widget for that purpose:

def receive_structure(evt = None):
    print(evt.text.split("\n")[:10])

AjaxCommunication("https://files.rcsb.org/view/%s.pdb" % pdb_code, receive_structure)()

pdb_code variable provides the code of a protein to be acquired (e.g. 2gb1) and receive_structure() is the callback method that is called when AjaxCommunication finally receives the data. The protein comes as text (in the PDB) format and it’s receive_structure() responsibility to process it further. Here it just breaks the text into lines and prints the top 10 lines of the file.

References

[1]	https://inkscape.org